The federal government will block a ship of 65,000 live sheep and 250 cattle bound for the Middle East if the export company fails to meet stringent new conditions.
The agriculture department has written to Emanuel Exports saying footage showing live exports on one of its vessels suffering from heat stress and other poor conditions last year has raised "serious concerns" about animal welfare.
Agriculture Department Assistant Secretary Narelle Clegg wrote to Emanuel manager Nicholas Daws on Thursday, outlining the proposed conditions.
The department wants the amount of stock on the ship to be reduced, and independently gathered video and photographs of conditions sent to the department daily after it sets sail.
Stocking density, food and water regimes and ventilation are also included in its concerns.
In the letter, Ms Clegg said new information had shown previous evidence of overcrowding and sheep which could not readily access food and water on Emanuel vessels "over a period in 2017".
The new information had shown sheep were bogged in their own waste which compounded heat stress, while sick and injured animals were not treated or euthanised.
Emanuel will need departmental approval to export its current shipment, which is due to leave Australia for Kuwait, United Arab Emirates, Oman and Qatar on Tuesday.
Footage of a shipment from August last year is expected be shown on Channel Nine's 60 Minutes program on Sunday night.
About 2400 sheep died on the 2017 voyage, with Agriculture Minister David Littleproud on Thursday announcing an investigation into the shipping company's practices.
He said he was "shocked and deeply disturbed" by the footage and would take strong action against anyone not fulfilling their responsibilities.